diff options
| -rw-r--r-- | benchmarks.csv | 40 | ||||
| -rw-r--r-- | lj_matrix.py | 20 | ||||
| -rw-r--r-- | main.py | 56 |
3 files changed, 68 insertions, 48 deletions
diff --git a/benchmarks.csv b/benchmarks.csv index 181da4e77..eb0ff0333 100644 --- a/benchmarks.csv +++ b/benchmarks.csv @@ -1,17 +1,23 @@ -ml_type,tr_size,te_size,sigma,mae,time -CM,2500,1500,1000.0,26.97361909951274,282.1443384 -L-JM,2500,1500,1000.0,11.785532138202667,277.3047686 -CM,3000,1500,1000.0,24.641045831013365,368.9830951 -L-JM,3000,1500,1000.0,11.08713556535848,370.8802103 -CM,3500,1500,1000.0,23.152765029544195,467.1278212 -L-JM,3500,1500,1000.0,10.430573100461325,464.2503922 -CM,4000,1500,1000.0,22.15854674774742,562.7823053 -L-JM,4000,1500,1000.0,10.117842321543852,564.9598646000001 -CM,4500,1500,1000.0,21.180935112846054,655.8574701 -L-JM,4500,1500,1000.0,9.677330400431318,652.4534939 -CM,5000,1500,1000.0,20.30113013118839,755.6121498 -L-JM,5000,1500,1000.0,9.143465812164308,759.3658756 -CM,5500,1500,1000.0,19.749349939851125,867.1811531999999 -L-JM,5500,1500,1000.0,8.902193965087893,863.8858544000001 -CM,6000,1101,1000.0,18.989775833821966,934.9760266999999 -L-JM,6000,1101,1000.0,8.595942764490113,932.6673659 +ml_type,tr_size,te_size,kernel_s,mae,time,lj_s,lj_e,date_ran +CM,1500,1500,1000.0,31.512240475332977,100.3640273,na,na,14/12/2019 +L-JM,1500,1500,1000.0,14.071581760048153,101.6336081,1,1,14/12/2019 +CM,2000,1500,1000.0,28.245321081132253,152.88077109999998,na,na,14/12/2019 +L-JM,2000,1500,1000.0,12.641839980374655,155.5011396,1,1,14/12/2019 +CM,2500,1500,1000.0,26.97361909951274,215.9536518,na,na,14/12/2019 +L-JM,2500,1500,1000.0,11.785532138202667,211.8681615,1,1,14/12/2019 +CM,3000,1500,1000.0,24.641045831013365,278.5150912,na,na,14/12/2019 +L-JM,3000,1500,1000.0,11.08713556535848,278.5971606,1,1,14/12/2019 +CM,3500,1500,1000.0,23.152765029544195,401.9234568,na,na,14/12/2019 +L-JM,3500,1500,1000.0,10.430573100461325,408.3161812,1,1,14/12/2019 +CM,4000,1500,1000.0,22.15854674774742,499.55023489999996,na,na,14/12/2019 +L-JM,4000,1500,1000.0,10.117842321543852,503.7487102,1,1,14/12/2019 +CM,4500,1500,1000.0,21.180935112846054,605.4631191999999,na,na,14/12/2019 +L-JM,4500,1500,1000.0,9.677330400431318,604.4122219,1,1,14/12/2019 +CM,5000,1500,1000.0,20.30113013118839,699.0641616,na,na,14/12/2019 +L-JM,5000,1500,1000.0,9.143465812164308,701.9964291,1,1,14/12/2019 +CM,5500,1500,1000.0,19.749349939851125,816.2225933,na,na,14/12/2019 +L-JM,5500,1500,1000.0,8.902193965087893,800.8945613,1,1,14/12/2019 +CM,6000,1101,1000.0,18.989775833821966,894.5558989,na,na,14/12/2019 +L-JM,6000,1101,1000.0,8.595942764490113,885.4234397,1,1,14/12/2019 +CM,6500,601,1000.0,19.424238707695146,956.2706457,na,na,14/12/2019 +L-JM,6500,601,1000.0,8.636351001125403,950.2348745,1,1,14/12/2019 diff --git a/lj_matrix.py b/lj_matrix.py index 5cb1b5a8d..2a8e0d956 100644 --- a/lj_matrix.py +++ b/lj_matrix.py @@ -29,6 +29,8 @@ from numpy.linalg import eig def lj_matrix(mol_data, nc_data, + sigma=1.0, + epsilon=1.0, max_len=25, as_eig=True, bohr_radius_units=False): @@ -92,11 +94,11 @@ def lj_matrix(mol_data, # Conversion factor is included in r^2. # 1/r^2 - r_2 = 1/(conversion_rate**2*(x + y + z)) + r_2 = sigma**2/(conversion_rate**2*(x + y + z)) r_6 = math.pow(r_2, 3) r_12 = math.pow(r_6, 2) - lj[i, j] = (4*(r_12 - r_6)) + lj[i, j] = (4*epsilon*(r_12 - r_6)) else: break @@ -150,11 +152,11 @@ def lj_matrix(mol_data, # Conversion factor is included in r^2. # 1/r^2 - r_2 = 1/(conversion_rate**2*(x + y + z)) + r_2 = sigma**2/(conversion_rate**2*(x + y + z)) r_6 = math.pow(r_2, 3) r_12 = math.pow(r_6, 2) - lj_row.append(4*(r_12 - r_6)) + lj_row.append(4*epsilon*(r_12 - r_6)) lj_temp.append(np.array(lj_row)) @@ -169,6 +171,8 @@ def lj_matrix(mol_data, def lj_matrix_multiple(mol_data, nc_data, pipe=None, + sigma=1, + epsilon=1, max_len=25, as_eig=True, bohr_radius_units=False): @@ -185,7 +189,13 @@ def lj_matrix_multiple(mol_data, printc('L-J Matrices calculation started.', 'CYAN') tic = time.perf_counter() - ljm_data = np.array([lj_matrix(mol, nc, max_len, as_eig, bohr_radius_units) + ljm_data = np.array([lj_matrix(mol, + nc, + sigma, + epsilon, + max_len, + as_eig, + bohr_radius_units) for mol, nc in zip(mol_data, nc_data)]) toc = time.perf_counter() @@ -43,37 +43,37 @@ def main(): procs = [] pipes = [] - cm_recv, cm_send = Pipe(False) - p1 = Process(target=c_matrix_multiple, - args=(molecules, nuclear_charge, cm_send)) - procs.append(p1) - pipes.append(cm_recv) - p1.start() + # cm_recv, cm_send = Pipe(False) + # p1 = Process(target=c_matrix_multiple, + # args=(molecules, nuclear_charge, cm_send)) + # procs.append(p1) + # pipes.append(cm_recv) + # p1.start() ljm_recv, ljm_send = Pipe(False) p2 = Process(target=lj_matrix_multiple, - args=(molecules, nuclear_charge, ljm_send)) + args=(molecules, nuclear_charge, ljm_send, 1.5)) procs.append(p2) pipes.append(ljm_recv) p2.start() - cm_data = pipes[0].recv() - ljm_data = pipes[1].recv() + # cm_data = pipes[0].recv() + ljm_data = pipes[0].recv() for proc in procs: proc.join() # ML calculation. procs = [] - cm_pipes = [] + # cm_pipes = [] ljm_pipes = [] - for i in range(2500, 6000 + 1, 500): - cm_recv, cm_send = Pipe(False) - p1 = Process(target=do_ml, - args=(cm_data, energy_pbe0, i, 'CM', cm_send)) - procs.append(p1) - cm_pipes.append(cm_recv) - p1.start() + for i in range(1500, 6500 + 1, 500): + # cm_recv, cm_send = Pipe(False) + # p1 = Process(target=do_ml, + # args=(cm_data, energy_pbe0, i, 'CM', cm_send)) + # procs.append(p1) + # cm_pipes.append(cm_recv) + # p1.start() ljm_recv, ljm_send = Pipe(False) p2 = Process(target=do_ml, @@ -82,21 +82,25 @@ def main(): ljm_pipes.append(ljm_recv) p2.start() - cm_bench_results = [] + # cm_bench_results = [] ljm_bench_results = [] - for cd_pipe, ljd_pipe in zip(cm_pipes, ljm_pipes): - cm_bench_results.append(cd_pipe.recv()) + for ljd_pipe in ljm_pipes: # cd_pipe, ljd_pipe in zip(cm_pipes, ljm_pipes): + # cm_bench_results.append(cd_pipe.recv()) ljm_bench_results.append(ljd_pipe.recv()) for proc in procs: proc.join() - with open('benchmarks.csv', 'w') as save_file: - save_file.write('ml_type,tr_size,te_size,sigma,mae,time\n') - for cm, ljm, in zip(cm_bench_results, ljm_bench_results): - cm_text = ','.join([str(field) for field in cm]) + '\n' - ljm_text = ','.join([str(field) for field in ljm]) + '\n' - save_file.write(cm_text) + with open('benchmarks.csv', 'a') as save_file: + # save_file.write(''.join(['ml_type,tr_size,te_size,kernel_s,', + # 'mae,time,lj_s,lj_e,date_ran\n'])) + date = '/'.join([str(field) for field in time.localtime()[:3][::-1]]) + for ljm in ljm_bench_results: # cm, ljm, in zip(cm_bench_results, ljm_bench_results): + # cm_text = ','.join([str(field) for field in cm])\ + # + ',' + date + '\n' + ljm_text = ','.join([str(field) for field in ljm])\ + + ',1.5,1,' + date + '\n' + # save_file.write(cm_text) save_file.write(ljm_text) # End of program |